From 7fc34ea47526bfd5e23441fc00d9149ee13d3089 Mon Sep 17 00:00:00 2001
From: davor <vorgrimmlerdavid@gmx.de>
Date: Thu, 29 Oct 2015 13:33:30 +0000
Subject: Added molecular weight to compound and mg conversions

Added tests
---
 lib/compound.rb  | 33 +++++++++++++++++++++++++++++++++
 test/compound.rb | 14 ++++++++++++++
 2 files changed, 47 insertions(+)

diff --git a/lib/compound.rb b/lib/compound.rb
index a26528b..a86d2e6 100644
--- a/lib/compound.rb
+++ b/lib/compound.rb
@@ -21,6 +21,7 @@ module OpenTox
     field :png_id, type: BSON::ObjectId
     field :svg_id, type: BSON::ObjectId
     field :sdf_id, type: BSON::ObjectId
+    field :molecular_weight, type: Float
     field :fingerprints, type: Hash, default: {}
     field :default_fingerprint_size, type: Integer
 
@@ -325,6 +326,38 @@ module OpenTox
       $mongo["compounds"].aggregate(aggregate).collect{ |r| [r["_id"], r["tanimoto"]] }
         
     end
+    
+    ## TODO: Should the following conversion functions are in overwrite.rb:class Numeric?!
+    # Get mg from logmmol (for nch LOAEL/pTD50 data)
+    # @return [Float] value in mg
+    def logmmol_to_mg(value, mw)
+      mg = (10**(-1.0*value.to_f)*(mw.to_f*1000))
+      return mg
+    end
+
+   # Get mg from mmol
+   # @return [Float] value in mg
+   def mmol_to_mg(value, mw)
+      mg = (value.to_f)*(mw.to_f)
+      return mg
+    end
+
+   # Get mg from logmg
+   # @return [Float] value in mg
+   def logmg_to_mg(value)
+      mg = 10**value.to_f
+      return mg
+    end
+    
+    # Calculate molecular weight of Compound with OB and store it in object
+    # @return [Float] molecular weight
+    def molecular_weight
+      if self["molecular_weight"]==0.0 || self["molecular_weight"].nil?
+        update(:molecular_weight => OpenTox::Algorithm::Descriptor.physchem(self, ["Openbabel.MW"]).first)
+      end
+      self["molecular_weight"]
+    end
+
 
     private
 
diff --git a/test/compound.rb b/test/compound.rb
index 22c152b..3857a85 100644
--- a/test/compound.rb
+++ b/test/compound.rb
@@ -174,4 +174,18 @@ print c.sdf
       p neighbors
     end
   end
+
+  def test_molecular_weight
+    c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C"
+    assert_equal 100.15888, c.molecular_weight
+  end
+
+  def test_mg_conversions
+    c = OpenTox::Compound.from_smiles "O"
+    mw = c.molecular_weight
+    assert_equal 18.01528, mw
+    assert_equal 0.8105107141417474, c.logmmol_to_mg(4.34688225631145, mw)
+    assert_equal 9007.64, c.mmol_to_mg(500, mw)
+    assert_equal 2437.9999984148976, c.logmg_to_mg(3.387033701)
+  end
 end
-- 
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